fix: clear() now properly resets VFS and COW state

Bug: After brain.clear(), VFS operations failed with
"Source entity 00000000-0000-0000-0000-000000000000 not found"

Root causes fixed:
- VFS instance remained in memory pointing to deleted root entity
- FileSystemStorage.clear() set blobStorage=undefined but didn't reinit
- Write-through cache returned stale entity data after clear()

Changes:
- Re-initialize COW (BlobStorage) after storage.clear() in brainy.ts
- Reset and reinitialize VFS following checkout() pattern
- Add clearWriteCache() to BaseStorage, call in Memory/FileSystem adapters
- Add 7 integration tests for VFS clear functionality

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/brainy.ts

@@ -2638,6 +2638,34 @@ export class Brainy<T = any> implements BrainyInterface<T> {
       this._neural = undefined
       this._nlp = undefined
       this._tripleIntelligence = undefined
+
+      // v7.3.1: Re-initialize COW (BlobStorage) after storage.clear()
+      // storage.clear() sets blobStorage=undefined for FileSystem/cloud adapters
+      // VFS depends on blobStorage being available (unified blob storage for all files)
+      // Must be done BEFORE VFS reinitialization
+      if (typeof (this.storage as any).initializeCOW === 'function') {
+        await (this.storage as any).initializeCOW({
+          branch: (this.config.storage as any)?.branch || 'main',
+          enableCompression: true
+        })
+      }
+
+      // v7.3.1: Reset VFS state - root entity was deleted by storage.clear()
+      // Bug: VFS instance remained in memory pointing to deleted root entity
+      // Following checkout() pattern exactly (see lines 2907-2914)
+      if (this._vfs) {
+        // Clear PathResolver caches (including UnifiedCache VFS entries)
+        if ((this._vfs as any).pathResolver?.invalidateAllCaches) {
+          (this._vfs as any).pathResolver.invalidateAllCaches()
+        }
+        // Recreate and reinitialize VFS so it's ready for use
+        this._vfs = new VirtualFileSystem(this)
+        await this._vfs.init()
+        // _vfsInitialized remains true since we just initialized
+      } else {
+        // VFS was never used, reset flag for clean state
+        this._vfsInitialized = false
+      }
     })
   }
 

src/storage/adapters/fileSystemStorage.ts

@@ -1039,6 +1039,11 @@ export class FileSystemStorage extends BaseStorage {
     // These in-memory counters must be reset to 0 after clearing all data
     ;(this as any).totalNounCount = 0
     ;(this as any).totalVerbCount = 0
+
+    // v7.3.1: Clear write-through cache (inherited from BaseStorage)
+    // Without this, readWithInheritance() would return stale cached data
+    // after clear(), causing "ghost" entities to appear
+    this.clearWriteCache()
   }
 
   /**

src/storage/adapters/memoryStorage.ts

@@ -160,6 +160,7 @@ export class MemoryStorage extends BaseStorage {
   /**
    * Clear all data from storage
    * v5.4.0: Clears objectStore (type-first paths)
+   * v7.3.1: Also clears writeCache to prevent stale data after clear
    */
   public async clear(): Promise<void> {
     this.objectStore.clear()
@@ -172,6 +173,11 @@ export class MemoryStorage extends BaseStorage {
     // Clear the statistics cache
     this.statisticsCache = null
     this.statisticsModified = false
+
+    // v7.3.1: Clear write-through cache (inherited from BaseStorage)
+    // Without this, readWithInheritance() would return stale cached data
+    // after clear(), causing "ghost" entities to appear
+    this.clearWriteCache()
   }
 
   /**

src/storage/baseStorage.ts

@@ -155,6 +155,16 @@ export abstract class BaseStorage extends BaseStorageAdapter {
   // Memory footprint: Bounded by batch size (typically <1000 items during imports)
   private writeCache = new Map<string, any>()
 
+  /**
+   * v7.3.1: Clear the write-through cache
+   * MUST be called by all storage adapter clear() implementations to ensure
+   * read-after-write consistency cache doesn't return stale data after clear.
+   * @protected - Available to subclasses for clear() implementation
+   */
+  protected clearWriteCache(): void {
+    this.writeCache.clear()
+  }
+
   // COW (Copy-on-Write) support - v5.0.0
   public refManager?: RefManager
   public blobStorage?: BlobStorage